The first predecessor of the squadron was organized during World War II as the 9th Reconnaissance Squadron. Redesignated the 399th Bombardment Squadron, it served as a crew training unit until inactivated in May 1944.
The 99th Air Refueling Squadron was activated in July 1957 and served with Strategic Air Command (SAC) until 1973, and again from 1983. In 1985, it was consolidated with the 399th Bombardment Squadron. When SAC was inactivated in 1992, the squadron became an element of Air Mobility Command. The squadron was inactivated in 2008, but was reactivated as an associated unit the following year.
The earliest predecessor of the squadron was constituted in January 1942 as the 9th Reconnaissance Squadron. However, the squadron was redesignated as the 399th Bombardment Squadron before activating on paper at Salt Lake City Army Air Base, Utah as one of the original four squadrons of the 88th Bombardment Group.
In September the squadron moved to Geiger Field, Washington, then to Walla Walla Army Air Base, Washington and received its first personnel and Boeing B-17 Flying Fortresses and became a heavy bomber Operational Training Unit (OTU) under II Bomber Command. The OTU program involved the use of an oversized parent unit to provide cadres to "satellite groups." The squadron's time as an OTU was brief and it soon became a Replacement Training Unit (RTU). Like OTUs, RTUs were also oversized units, but their mission was to train individual pilots or aircrews.
In November 1943 the squadron moved to Avon Park Army Air Field, Florida and became part of III Bomber Command, as Second Air Force concentrated on training Boeing B-29 Superfortress aircrews. However, the Army Air Forces found that standard military units, based on relatively inflexible tables of organization, were not proving well adapted to the training mission. Accordingly, it adopted a more functional system in which each base was organized into a separate numbered unit, while the groups and squadrons like the 399th acting as RTUs were disbanded or inactivated in the spring of 1944.